Explorer for Integrated Cantley Atlas + Curated Kinase-Substrate Interactions

Author

Chinmaya Joisa

Published

September 8, 2025

Curated kinase–substrate network, ready to explore

Seed the graph with a kinase and/or substrate, filter on functional evidence, and export images or tables for publication.

Kinases

—

Substrates

—

Interactions

—

Curated share

—

Network

Choose seeds, then explore

Kinase: Kinase seed Substrate: Substrate seed Layout: Node labels Edge labels Arrows Only functional Label size: 100%

Kinase Substrate Known (curated) Novel (Cantley) Dotted = not flagged functional; Solid = likely functional

Tip: start with a single kinase or substrate to see its neighborhood; toggle layouts to untangle dense regions.

Edges in View

Filter columns or download

--- title: "Explorer for Integrated Cantley Atlas + Curated Kinase-Substrate Interactions" editor: visual author: "Chinmaya Joisa" date: "09/08/2025" toc: true toc-depth: 5 toc-title: Table of Contents highlight-style: pygments format: html: embed-resources: true code-fold: true code-tools: true execute: echo: false cache: false message: false warning: false out-width: "100%" fig-align: center fig-dpi: 300 --- ```{r setup, include=FALSE, cache = FALSE} require("knitr") knitr::opts_knit$set(root.dir = here::here()) set.seed(123) ``` ```{r load_libraries, message=FALSE, warning=FALSE} library(tidyverse) library(tidygraph) library(here) library(org.Hs.eg.db) library(clusterProfiler) library(igraph) library(ggraph) library(scales) library(readxl) library(ggpubr) library(jsonlite) library(htmltools) library(ggupset) library(patchwork) combined_pairs = read_csv(here("results/combined_kinase_substrate_pairs_2025.csv")) ``` ```{r, echo=FALSE, results='asis'} curated_sources <- c("PhosphoSitePlus","EPSD","iPTMNet","PhosphoELM","PhosphoNetworks") edge_tbl <- combined_pairs %>% mutate(evidence = if_else(Source %in% curated_sources, "Known (curated)", "Novel (Cantley)")) %>% group_by(Kinase, Substrate) %>% summarise( evidence = if_else(any(evidence == "Known (curated)"), "Known (curated)", "Novel (Cantley)"), Likely_functional = any(Likely_functional), SiteCount = n_distinct(Site), Sites = paste(sort(unique(na.omit(Site))), collapse = "; "), Reference_PMID = paste(sort(unique(Reference_PMID[!is.na(Reference_PMID) & Reference_PMID != ""])), collapse = "; "), Sources = paste(sort(unique(Source)), collapse = "; "), .groups = "drop" ) %>% transmute( source = Kinase, target = Substrate, evidence, Likely_functional, SiteCount, Sites, Reference_PMID, edgeLabel = paste0(evidence, ifelse(Likely_functional, " · functional", "")), SourceList = Sources ) %>% mutate(Likely_functional = if_else(Likely_functional, "Likely functional", "Other/Unknown")) node_tbl <- bind_rows( combined_pairs %>% transmute(Gene = Kinase, Entrez = Kinase_entrez, role = "Kinase"), combined_pairs %>% transmute(Gene = Substrate, Entrez = Substrate_entrez, role = "Substrate") ) %>% mutate(Entrez = if_else(is.na(Entrez) | Entrez == "", NA_integer_, Entrez)) %>% group_by(Gene) %>% summarise( Entrez = dplyr::first(na.omit(Entrez)), role = paste(sort(unique(role)), collapse = ","), .groups = "drop" ) %>% arrange(Gene) deg_tbl <- edge_tbl %>% count(source, name = "outdeg") %>% full_join(edge_tbl %>% count(target, name = "indeg"), by = c("source" = "target")) %>% mutate(outdeg = coalesce(outdeg, 0L), indeg = coalesce(indeg, 0L)) %>% transmute(Gene = source, outdeg, indeg) %>% distinct() #add uniprot ID to node_tbl (convert from entrezid) node_uniprot = bitr(node_tbl$Entrez, fromType="ENTREZID", toType="UNIPROT", OrgDb="org.Hs.eg.db") node_tbl <- node_tbl %>% left_join(deg_tbl, by = "Gene") %>% mutate(Entrez = as.character(Entrez)) %>% left_join(node_uniprot, by = c("Entrez" = "ENTREZID")) %>% mutate(outdeg = coalesce(outdeg, 0L), indeg = coalesce(indeg, 0L)) nodes_json <- node_tbl %>% transmute(data = pmap(list(id = Gene, label = Gene, Entrez = Entrez, role = role, indeg = indeg, outdeg = outdeg, deg = indeg + outdeg, uniprot = UNIPROT), ~ list(id = ..1, label = ..2, Entrez = ..3, role = ..4, indeg = ..5, outdeg = ..6, deg = ..7, uniprot = ..8))) %>% tidyr::unnest_wider(data) edges_json <- edge_tbl %>% transmute(data = pmap(list(source, target, evidence, Likely_functional, SiteCount, Sites, Reference_PMID, edgeLabel, SourceList), ~ list(source = ..1, target = ..2, evidence = ..3, Likely_functional = ..4, SiteCount = ..5, Sites = ..6, Reference_PMID = ..7, edgeLabel = ..8, SourceList = ..9))) %>% tidyr::unnest_wider(data) payload <- list(nodes = nodes_json, edges = edges_json) json_payload <- jsonlite::toJSON(payload, auto_unbox = TRUE) json_kinases <- jsonlite::toJSON(sort(node_tbl$Gene[grepl("Kinase", node_tbl$role, fixed = TRUE)]), auto_unbox = TRUE) json_subs <- jsonlite::toJSON(sort(node_tbl$Gene[grepl("Substrate", node_tbl$role, fixed = TRUE)]), auto_unbox = TRUE) ``` ```{r} data_tags <- tagList( tags$script(id = "ks-data", type = "application/json", HTML(json_payload)), tags$script(id = "kin-data", type = "application/json", HTML(json_kinases)), tags$script(id = "sub-data", type = "application/json", HTML(json_subs)) ) viewer_tags <- tags$div( `data-quarto-disable-processing` = "true", tags$style(HTML(" @import url('https://fonts.googleapis.com/css2?family=Space+Grotesk:wght@400;600;700&family=Manrope:wght@400;600&display=swap'); :root { --bg: #f5f1e6; --panel: #f0ece2; --panel-2: #e8e3d8; --ink: #1f1b16; --muted: #5b564c; --accent: #2f2a24; --accent-2: #4b4336; --stroke: rgba(0,0,0,0.12); --card-shadow: 0 10px 30px rgba(0,0,0,0.08); } body {font-family:'Manrope', 'Space Grotesk', sans-serif; background: repeating-linear-gradient(0deg, #f5f1e6 0px, #f5f1e6 18px, #f2ede3 18px, #f2ede3 36px); color: var(--ink);} .page-shell{max-width:1200px;margin:0 auto;padding:24px 18px 42px;} header#topbar{display:flex;align-items:center;justify-content:space-between;padding:14px 16px;margin-bottom:14px;border:1px solid var(--stroke);background:linear-gradient(120deg, rgba(0,0,0,0.02), rgba(0,0,0,0.01));border-radius:14px;box-shadow:var(--card-shadow);backdrop-filter: blur(2px);position:sticky;top:0;z-index:10} #brand{display:flex;align-items:center;gap:10px;font-weight:700;font-size:18px;letter-spacing:0.4px;text-transform:uppercase;color:var(--ink)} #brand .dot{width:10px;height:10px;border-radius:50%;background:var(--accent-2);box-shadow:none} nav a{color:var(--muted);text-decoration:none;margin-left:16px;font-weight:600;font-size:13px;padding:6px 10px;border-radius:10px;border:1px solid transparent} nav a:hover{color:var(--ink);border-color:var(--stroke);background:rgba(0,0,0,0.03)} #hero{padding:22px 20px 18px;border:1px solid var(--stroke);border-radius:18px;background:linear-gradient(140deg, rgba(0,0,0,0.02), rgba(0,0,0,0.05));box-shadow:var(--card-shadow);margin-bottom:20px} #hero h1{margin:0 0 10px;font-size:26px;letter-spacing:0.2px} #hero p{margin:0;color:var(--muted)} .stat-row{display:flex;gap:12px;flex-wrap:wrap;margin-top:14px} .stat{flex:1 1 160px;border:1px solid var(--stroke);background:var(--panel);border-radius:14px;padding:10px 12px} .stat .label{font-size:12px;color:var(--muted);text-transform:uppercase;letter-spacing:0.5px} .stat .value{font-size:20px;font-weight:700;color:var(--ink)} .section-head{display:flex;align-items:center;justify-content:space-between;margin:18px 2px 10px} .section-head h3{margin:0;font-size:18px} .section-head .pill{font-size:12px;padding:4px 8px;border-radius:999px;border:1px solid var(--stroke);color:var(--muted)} .panel{border:1px solid var(--stroke);background:var(--panel);border-radius:16px;padding:14px 14px 10px;box-shadow:var(--card-shadow)} #controls{display:flex;gap:10px;flex-wrap:wrap;align-items:center} #exportbar{display:flex;gap:10px;flex-wrap:wrap;margin:10px 0 10px 0} #legend{display:flex;gap:16px;flex-wrap:wrap;align-items:center;margin:4px 0 8px 0;font-size:13px;color:var(--muted)} #legend .chip{display:inline-flex;align-items:center;gap:6px;padding:4px 6px;border-radius:10px;border:1px solid var(--stroke);background:var(--panel-2)} #legend .line{width:32px;height:0;border-top:3px solid #999} #legend .line.known{border-color:#1f1b16} #legend .line.novel{border-color:#5f564c} #legend .dot{width:14px;height:14px;border-radius:50%;display:inline-block;border:1px solid #444} #legend .kin{background:#f4efe4} #legend .sub{background:#e9e2d6} .legend-note{color:var(--muted)} #cywrap{margin-top:10px} #cy {width:100%;height:720px;border:1px solid var(--stroke);border-radius:12px;background:#f7f2e8} .label {font-weight:600;color:var(--muted)} .badge {display:inline-block;padding:2px 8px;border-radius:999px;margin-left:6px;border:1px solid var(--stroke);color:var(--muted);background:var(--panel-2)} .kbadge{background:#f4efe4;border-color:#3b352c;color:#1f1b16} .sbadge{background:#e9e2d6;border-color:#4a4339;color:#1f1b16} .tablewrap{margin-top:12px} .filters {display:flex;gap:8px;flex-wrap:wrap;margin:8px 0} .filters input {padding:8px 10px;border:1px solid var(--stroke);border-radius:10px;font-size:13px;background:var(--panel);color:var(--ink)} .filters input:focus{outline:1px solid var(--accent)} .tablebox {max-height:400px; overflow:auto; border:1px solid var(--stroke); border-radius:12px;background:var(--panel-2)} .tbl {border-collapse:collapse;width:100%} .tbl th, .tbl td{border-bottom:1px solid var(--stroke);padding:8px 10px;font-size:13px;text-align:left;white-space:nowrap;color:var(--ink)} .tbl th{background:rgba(0,0,0,0.02); position: sticky; top: 0; z-index: 1; color:var(--muted)} .btn{padding:8px 12px;border:1px solid var(--stroke);border-radius:10px;background:linear-gradient(120deg, rgba(0,0,0,0.02), rgba(0,0,0,0.04));cursor:pointer;color:var(--ink);font-weight:600} .btn:hover{background:linear-gradient(120deg, rgba(0,0,0,0.05), rgba(0,0,0,0.07))} .btn.primary{border-color:var(--accent);box-shadow:none} .tip{margin:10px 0 4px;border:1px dashed var(--stroke);border-radius:10px;padding:8px 10px;font-size:13px;color:var(--muted);background:rgba(0,0,0,0.02)} select, input[type='checkbox'], input[list]{background:var(--panel-2);color:var(--ink);border:1px solid var(--stroke);border-radius:8px;padding:6px 8px} select{padding:8px 10px} input[list]{min-width:220px} @media (max-width: 768px){#controls{flex-direction:column;align-items:flex-start} #cy{height:520px}} ")), tags$div( class="page-shell", tags$header(id="topbar", tags$div(id="brand", tags$span(class="dot"), "KinaseCanvas Explorer"), tags$nav( tags$a(href="#network", "Network"), tags$a(href="#table", "Edges"), tags$a(href="https://kinet.kinametrix.com/#section-proteins", target="_blank", "Reference") ) ), tags$section(id="hero", tags$h1("Curated kinase–substrate network, ready to explore"), tags$p("Seed the graph with a kinase and/or substrate, filter on functional evidence, and export images or tables for publication."), tags$div(class="stat-row", tags$div(class="stat", tags$div(class="label", "Kinases"), tags$div(id="statKinases", class="value", "—")), tags$div(class="stat", tags$div(class="label", "Substrates"), tags$div(id="statSubstrates", class="value", "—")), tags$div(class="stat", tags$div(class="label", "Interactions"), tags$div(id="statEdges", class="value", "—")), tags$div(class="stat", tags$div(class="label", "Curated share"), tags$div(id="statCurated", class="value", "—")) ) ), tags$section(id="network", class="section", tags$div(class="section-head", tags$h3("Network"), tags$span(class="pill", "Choose seeds, then explore")), tags$div(class="panel", tags$div( id = "controls", tags$label(class="label", "Kinase:", `for`="kinSel"), tags$input(id="kinSel", list="kinList", placeholder="Type a kinase…", style="min-width:240px"), tags$datalist(id="kinList"), tags$span(class="badge kbadge", "Kinase seed"), tags$label(class="label", "Substrate:", `for`="subSel", style="margin-left:12px"), tags$input(id="subSel", list="subList", placeholder="Type a substrate…", style="min-width:240px"), tags$datalist(id="subList"), tags$span(class="badge sbadge", "Substrate seed"), tags$label(class="label", "Layout:", `for`="layoutSel", style="margin-left:12px"), tags$select( id="layoutSel", tags$option(value="fcose","fCoSE"), tags$option(value="cose","COSE"), tags$option(value="cose-bilkent","CoSE-Bilkent"), tags$option(value="concentric","Concentric"), tags$option(value="breadthfirst","Breadthfirst") ), tags$label(tags$input(type="checkbox", id="labelsChk", checked=NA), " Node labels"), tags$label(tags$input(type="checkbox", id="edgeLabelsChk"), " Edge labels"), tags$label(tags$input(type="checkbox", id="arrowsChk", checked=NA), " Arrows"), tags$label(tags$input(type="checkbox", id="onlyFunctionalChk"), " Only functional"), tags$label(class="label", "Label size:", `for`="labelScale", style="margin-left:12px"), tags$input(type="range", id="labelScale", min="50", max="180", value="100", step="10", style="width:140px"), tags$span(id="labelScaleVal", class="badge", "100%") ), tags$div(id="legend", tags$span(class="chip", tags$span(class="dot kin"), "Kinase"), tags$span(class="chip", tags$span(class="dot sub"), "Substrate"), tags$span(class="chip", tags$span(class="line known"), "Known (curated)"), tags$span(class="chip", tags$span(class="line novel"), "Novel (Cantley)"), tags$span(class="legend-note", "Dotted = not flagged functional; Solid = likely functional") ), tags$div(class="tip", "Tip: start with a single kinase or substrate to see its neighborhood; toggle layouts to untangle dense regions."), tags$div(id="exportbar", tags$button(id="btnPng", class="btn primary", "Export PNG"), tags$button(id="btnPdf", class="btn", "Export PDF"), tags$button(id="btnCsvEdges", class="btn", "Download Edges CSV") ), tags$div(id="cywrap", tags$div(id="cy")) ) ), tags$section(id="table", class="section", tags$div(class="section-head", tags$h3("Edges in View"), tags$span(class="pill", "Filter columns or download")), tags$div(class="panel", tags$div(id="edgesFilters", class="filters"), tags$div(id="edgesTable", class="tablebox") ) ) ), tags$script(src="https://unpkg.com/cytoscape@3.26.0/dist/cytoscape.min.js"), tags$script(src="https://unpkg.com/layout-base/layout-base.js"), tags$script(src="https://unpkg.com/cose-base/cose-base.js"), tags$script(src="https://unpkg.com/cytoscape-fcose@2.2.0/cytoscape-fcose.js"), tags$script(src="https://unpkg.com/cytoscape-cose-bilkent@4.1.0/cytoscape-cose-bilkent.js"), tags$script(src="https://cdn.jsdelivr.net/npm/jspdf@2.5.1/dist/jspdf.umd.min.js"), tags$script(HTML(" (function(){ const data = JSON.parse(document.getElementById('ks-data').textContent); const kinases = JSON.parse(document.getElementById('kin-data').textContent); const substrates = JSON.parse(document.getElementById('sub-data').textContent); const maxDeg = data.nodes.reduce((m,n) => Math.max(m, (n.indeg || 0) + (n.outdeg || 0)), 0); const stats = { kinases: kinases.length, substrates: substrates.length, edges: data.edges.length, curated: data.edges.filter(e => e.evidence === 'Known (curated)').length }; const setStat = (id, text) => { const el = document.getElementById(id); if(el) el.textContent = text; }; setStat('statKinases', stats.kinases.toLocaleString()); setStat('statSubstrates', stats.substrates.toLocaleString()); setStat('statEdges', stats.edges.toLocaleString()); setStat('statCurated', stats.edges ? Math.round((stats.curated / stats.edges) * 100).toString() + '% curated' : '—'); const kinDL = document.getElementById('kinList'); kinases.forEach(g => { const opt = document.createElement('option'); opt.value = g; kinDL.appendChild(opt); }); const subDL = document.getElementById('subList'); substrates.forEach(g => { const opt = document.createElement('option'); opt.value = g; subDL.appendChild(opt); }); // default seeds so something renders immediately const kinInput = document.getElementById('kinSel'); const subInput = document.getElementById('subSel'); if(kinases.length){ kinInput.value = kinases[0]; } if(substrates.length){ subInput.placeholder = 'Type a substrate… (optional)'; } const labelScale = document.getElementById('labelScale'); const labelScaleEl = document.getElementById('labelScaleVal'); const baseFont = 9; const basePad = 5; const cy = cytoscape({ container: document.getElementById('cy'), elements: [], style: [ { selector: 'node', style: { 'shape': 'round-rectangle', 'background-color': '#f6f1e7', 'label': 'data(label)', 'font-size': 10, 'color': '#1f1b16', 'text-opacity': 1, 'text-wrap': 'wrap', 'text-max-width': '100px', 'min-zoomed-font-size': 6, 'text-margin-y': -2, 'text-halign': 'center', 'text-valign': 'center', 'border-color': '#2f281e', 'border-width': 0.9, 'width': 'label', 'height': 'label', 'padding': '4px' } }, { selector: 'node[role *= \"Substrate\"]:not([role *= \"Kinase\"])', style: { 'background-color': '#e1d7c7', 'border-color': '#6a5c4a' } }, { selector: 'node[role *= \"Kinase\"]', style: { 'background-color': '#fbf6ec', 'border-color': '#2a241b' } }, { selector: 'node.qk', style: { 'border-width': 2.5 } }, { selector: 'node.qs', style: { 'border-width': 2.5 } }, { selector: 'edge', style: { 'width': 1.6, 'curve-style': 'bezier', 'line-color': '#4f4a42', 'target-arrow-color': '#4f4a42', 'target-arrow-shape': 'triangle', 'label': 'data(edgeLabel)', 'font-size': 9, 'text-rotation': 'autorotate', 'text-background-color': '#ffffff', 'text-background-opacity': 0.85, 'text-background-padding': 2, 'text-margin-y': -2 } }, { selector: 'edge[evidence = \"Known (curated)\"]', style: { 'line-color': '#16110c', 'target-arrow-color': '#16110c' } }, { selector: 'edge[evidence = \"Novel (Cantley)\"]', style: { 'line-color': '#7b6d5d', 'target-arrow-color': '#7b6d5d' } }, { selector: 'edge[Likely_functional = \"Likely functional\"]', style: { 'line-style': 'solid' } }, { selector: 'edge[Likely_functional = \"Other/Unknown\"]', style: { 'line-style': 'dotted' } } ], layout: { name: 'fcose' } }); cy.on('tap', 'node', evt => { const up = (evt.target && evt.target.data) ? evt.target.data('uniprot') : null; if(!up) return; const url = 'https://www.uniprot.org/uniprotkb/' + encodeURIComponent(up); window.open(url, '_blank', 'noopener'); }); function setNodeLabels(show){ cy.style().selector('node').style('label', show ? 'data(label)' : '').update(); } function setEdgeLabels(show){ cy.style().selector('edge').style('label', show ? 'data(edgeLabel)' : '').update(); } function setArrows(show){ cy.style().selector('edge').style('target-arrow-shape', show ? 'triangle' : 'none').update(); } function applyNodeSizing(){ const scale = Number(labelScale.value || 100) / 100; if(labelScaleEl){ labelScaleEl.textContent = Math.round(scale * 100) + '%'; } cy.batch(() => { cy.nodes().forEach(n => { const fontSize = Math.max(7, Math.min(14, baseFont * scale)); const pad = Math.max(3, Math.min(12, basePad * scale)); n.style({ 'font-size': fontSize, 'padding': pad }); }); }); } function isFunctionalEdge(e){ const v = (e.data('Likely_functional') ?? '').trim(); return v === 'Likely functional'; } function applyFunctionalFilter(onlyFunctional){ if(!onlyFunctional){ cy.edges().style('display', 'element'); cy.nodes().style('display', 'element'); } else { cy.edges().forEach(e => { e.style('display', isFunctionalEdge(e) ? 'element' : 'none'); }); cy.nodes().forEach(n => { const hasVisibleEdge = n.connectedEdges(':visible').length > 0; n.style('display', hasVisibleEdge ? 'element' : 'none'); }); } relayout(document.getElementById('layoutSel').value); } function refreshEdgesTable(){ const rows = cy.edges(':visible').map(e => [ e.data('source'), e.data('target'), e.data('evidence'), e.data('Likely_functional'), e.data('SiteCount'), e.data('Sites'), e.data('SourceList') ?? '', e.data('Reference_PMID') ]); renderFilterableTable('edgesFilters','edgesTable', ['From','To','Evidence','Functional','#Sites','Sites','Sources','Reference_PMID'], rows); } function renderFilterableTable(filtersId, tableBoxId, headers, rows){ const fwrap = document.getElementById(filtersId); const box = document.getElementById(tableBoxId); fwrap.innerHTML = ''; box.innerHTML = ''; const filters = headers.map(h => { const inp = document.createElement('input'); inp.type = 'text'; inp.placeholder = 'Filter ' + h; fwrap.appendChild(inp); return inp; }); const table = document.createElement('table'); table.className = 'tbl'; const thead = document.createElement('thead'); const trh = document.createElement('tr'); headers.forEach(h => { const th = document.createElement('th'); th.textContent = h; trh.appendChild(th); }); thead.appendChild(trh); table.appendChild(thead); const tbody = document.createElement('tbody'); table.appendChild(tbody); box.appendChild(table); function passes(row, query){ for(let i=0;i<query.length;i++){ const q = query[i]; if(q && !String(row[i] ?? '').toLowerCase().includes(q)) return false; } return true; } function draw(){ const q = filters.map(x => x.value.trim().toLowerCase()); tbody.innerHTML = ''; rows.forEach(r => { if(!passes(r, q)) return; const tr = document.createElement('tr'); r.forEach(v => { const td = document.createElement('td'); td.textContent = (v ?? '').toString(); tr.appendChild(td); }); tbody.appendChild(tr); }); } filters.forEach(inp => inp.addEventListener('input', draw)); draw(); } function incidentSubgraph(seeds){ const nodeIndex = new Map(data.nodes.map(n => [n.id, n])); const validSeeds = seeds.filter(s => nodeIndex.has(s)); if(!validSeeds.length){ return {nodes:[], edges:[]}; } const edges = data.edges.filter(e => validSeeds.includes(e.source) || validSeeds.includes(e.target)); if(!edges.length){ return {nodes:[], edges:[]}; } const nset = new Set(); edges.forEach(e => { nset.add(e.source); nset.add(e.target); }); const nodes = Array.from(nset).map(id => ({ data: nodeIndex.get(id), classes: (validSeeds.includes(id) ? (seeds[0]===id ? 'qk' : (seeds[1]===id ? 'qs' : '')) : '') })); return {nodes: nodes.map(n => ({ data: n.data, classes: n.classes })), edges: edges.map(e => ({ data: e }))}; } function relayout(name){ const opts = (name==='concentric') ? { name, minNodeSpacing: 20 } : (name==='breadthfirst') ? { name, directed: true, padding: 10 } : (name==='fcose') ? { name, quality: 'default', randomize: true, animate: false, animationDuration: 1000, fit: true, padding: 30, nodeDimensionsIncludeLabels: false, uniformNodeDimensions: false, packComponents: false, tile: true, samplingType: true, sampleSize: 25, nodeSeparation: 90, nodeRepulsion: node => 4500, idealEdgeLength: edge => 80, edgeElasticity: edge => 0.45, nestingFactor: 0.1, numIter: 2500, gravity: 0.25, gravityRangeCompound: 1.5, gravityCompound: 1.0, gravityRange: 3.8, initialEnergyOnIncremental: 0.3 } : (name==='cose-bilkent') ? { name, animate: false, quality: 'draft', nodeRepulsion: 30000, idealEdgeLength: 140, gravity: 0.8, tile: true, nodeDimensionsIncludeLabels: true, padding: 30 } : { name: 'cose', animate: false }; cy.layout(opts).run(); } function render(){ const kin = document.getElementById('kinSel').value.trim(); const sub = document.getElementById('subSel').value.trim(); const seeds = [kin, sub].filter(s => s && s.length); if(!seeds.length) return; const elems = incidentSubgraph(seeds); cy.elements().remove(); cy.add(elems.nodes); cy.add(elems.edges); relayout(document.getElementById('layoutSel').value); applyNodeSizing(); const rows = cy.edges().map(e => [ e.data('source'), e.data('target'), e.data('evidence'), e.data('Likely_functional'), e.data('SiteCount'), e.data('Sites'), e.data('SourceList') ?? '', e.data('Reference_PMID') ]); renderFilterableTable('edgesFilters','edgesTable', ['From','To','Evidence','Functional','#Sites','Sites','Sources','Reference_PMID'], rows); const onlyFn = document.getElementById('onlyFunctionalChk').checked; applyFunctionalFilter(onlyFn); refreshEdgesTable(); } const triggerRender = () => render(); const triggerOnEnter = el => el.addEventListener('keyup', e => { if(e.key === 'Enter') render(); }); kinInput.addEventListener('change', triggerRender); subInput.addEventListener('change', triggerRender); triggerOnEnter(kinInput); triggerOnEnter(subInput); document.getElementById('layoutSel').addEventListener('change', () => render()); document.getElementById('labelsChk').addEventListener('change', e => setNodeLabels(e.target.checked)); document.getElementById('edgeLabelsChk').addEventListener('change', e => setEdgeLabels(e.target.checked)); document.getElementById('arrowsChk').addEventListener('change', e => setArrows(e.target.checked)); document.getElementById('onlyFunctionalChk').addEventListener('change', () => { applyFunctionalFilter(document.getElementById('onlyFunctionalChk').checked); refreshEdgesTable(); }); labelScale.addEventListener('input', applyNodeSizing); function download(filename, blob){ const a = document.createElement('a'); a.href = URL.createObjectURL(blob); a.download = filename; document.body.appendChild(a); a.click(); a.remove(); setTimeout(() => URL.revokeObjectURL(a.href), 5000); } function csvBlob(rows, header){ const esc = v => '\"' + String(v ?? '').replaceAll('\"','\"\"') + '\"'; const lines = [header.map(esc).join(',')].concat(rows.map(r => r.map(esc).join(','))); const newline = String.fromCharCode(10); const csv = lines.join(newline); return new Blob([csv], {type:'text/csv'}); } document.getElementById('btnPng').addEventListener('click', () => { const uri = cy.png({full:true, scale:2}); fetch(uri).then(r => r.blob()).then(b => download('kinome_network.png', b)); }); document.getElementById('btnPdf').addEventListener('click', () => { const uri = cy.png({full:true, scale:2}); fetch(uri).then(r => r.blob()).then(b => { const reader = new FileReader(); reader.onload = function(){ const { jsPDF } = window.jspdf; const pdf = new jsPDF({orientation:'landscape', unit:'pt', format:'a4'}); const img = reader.result; const pageW = pdf.internal.pageSize.getWidth(); const pageH = pdf.internal.pageSize.getHeight(); pdf.addImage(img, 'PNG', 20, 20, pageW-40, pageH-40); pdf.save('kinome_network.pdf'); }; reader.readAsDataURL(b); }); }); document.getElementById('btnCsvEdges').addEventListener('click', () => { const rows = cy.edges(':visible').map(e => [ e.data('source'), e.data('target'), e.data('evidence'), e.data('Likely_functional'), e.data('SiteCount'), e.data('Sites'), e.data('SourceList') ?? '', e.data('Reference_PMID') ]); const blob = csvBlob(rows, ['From','To','Evidence','Functional','#Sites','Sites','Sources','Reference_PMID']); download('kinome_edges.csv', blob); }); setNodeLabels(true); setEdgeLabels(false); setArrows(true); applyNodeSizing(); render(); })(); ")) ) browsable(tagList(data_tags, viewer_tags)) ```